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A Scientist's Nightmare: Software Problem Leads to Five Retractions

Greg Miller
2006 Science  
The structures of MsbA (purple) and Sav1866 (green) overlap little (left) until MsbA is inverted (right). SCIENCE VOL 314 22 DECEMBER 2006 A Scientist's Nightmare: Software Problem  ...  Leads to Five Retractions SCIENTIFIC PUBLISHING 180 ( 2006) L Published by AAAS on January 5, 2007 Downloaded from FOCUS Denser disk drives 1868 Controversial  ... 
doi:10.1126/science.314.5807.1856 pmid:17185570 fatcat:xwnkqs6w5jg55c6mus2t37uiiy


Nicolas Rougier, Konrad Hinsen
2018 Zenodo  
Nightmare: Software Problem Leads to Five Retractions Greg Miller.  ...  Article accessed online on March 28, 2017 No corrections, no warning, wrong results still online Cited by more than 2,000 papers Software Problem Leads to Five Retractions In September (2006) , Swiss  ... 
doi:10.5281/zenodo.4244850 fatcat:rgz725n5k5fmjgiezopfooqna4

ATPESC: Software Productivity 07: Testing, Code Coverage, and Continuous Integration [article]

Jared O'Neal, Alicia Klinvex
2018 Figshare  
Department of Energy Office of Science, Office of Advanced Scientific Computing Research (ASCR), and by the Exascale Computing Project (17-SC-20-SC), a collaborative effort of the U.S.  ...  : Software Problem Leads to Five Retractions".  ...  o One was cited 364 times • Many papers and grant applications conflicting with flawed results were rejected • Others based their research on incorrect results Greg Miller, "A Scientist's Nightmare  ... 
doi:10.6084/m9.figshare.6972749.v2 fatcat:genjegzym5an5di33nwopkphdy

Moving forward: Transparency, Openness, and Reproducibility in Our Lab

Bram Zandbelt, Guillaume Sescousse
2017 Figshare  
demise Indians wary of nuclear pact We really A Scientist's Nightmare: Software Problem Leads to Five Retractions SCIENTIFIC PUBLISHING CREDIT: R.  ...  +necessary+to+lead+a+group.++ + + + + Molecular Biology in 2003) and Salmonella typhimurium (published in Science in 2005).  ... 
doi:10.6084/m9.figshare.4877480 fatcat:5jge3h32nncidgq3ixf7sips3a

Misidentification of the Bray-Curtis similarity index

PM Yoshioka
2008 Marine Ecology Progress Series  
The BC and Cz indices differ because abundant species have the greatest impact on the Cz index, while all species (and samples) 'count the same' in the BC index, due to a double standardization of the  ...  The Bray-Curtis (BC) similarity index is misidentified in various software programs, and the index used by these programs is more appropriately credited to Czekanowski (Cz).  ...  John Wiley & Sons, New York Miller G (2006) A scientist's nightmare: software problem leads to five retractions. Science 314:1856-1857 Whittaker RH (1967) Gradient analysis of vegetation. Table 1.  ... 
doi:10.3354/meps07728 fatcat:2rvrid4n4fczhhslzzmznbv2m4

And the second shall be first

Gregory A Petsko
2007 Genome Biology  
The retraction of 5 protein crystal structures has held back an entire sub-field for years due to the inordinately persuasive power of the pretty pictures that structural biology produces.  ...  All too often the first report is sketchy, superficial in its analysis, and prone to error.  ...  corresponding atomic coordinate sets that had been published in Science, Molecular Biology, and Proceedings of the National Academy of Sciences (see Miller: A scientist's nightmare: software problem leads  ... 
doi:10.1186/gb-2007-8-2-103 pmid:17328789 pmcid:PMC1852413 fatcat:32ttoadpejdvnhxbrmimcvwvwa

Best Practices in Scientific Computing - Discussion of Wilson et al., PLos Biology, 2014 [article]

Bram Zandbelt
2017 Figshare  
A., Brown, C. T., Hong, N. P. C., Davis, M., Guy, R. T., ... & Waugh, B. (2014). Best practices for scientific computing. PLoS Biol, 12(1), e1001745.  ...  A Scientist's Nightmare: Software Problem Leads to Five Retractions SCIENTIFIC PUBLISHING CREDIT: R. J. P. DAWSON AND K. P.  ...  This can lead to serious errors impacting the central conclusions of published research [6] : recent high-profile retractions, technical comments, and corrections because of errors in computational methods  ... 
doi:10.6084/m9.figshare.4787812 fatcat:uweedjwdorh2fcowhzoqykzu5a

Supporting information for "BioDynaMo: a modular platform for high-performance agent-based simulation" [article]

Lukas Breitwieser, Ahmad Hesam, Jean de Montigny, Vasileios Vavourakis, Alexandros Iosif, Jack Jennings, Marcus Kaiser, Marco Manca, Alberto Di Meglio, Zaid Al-Ars, Fons Rademakers, Onur Mutlu (+1 others)
2020 Zenodo  
This repository contains all supporting material for the paper "BioDynaMo: a modular platform for high-performance agent-based simulation"  ...  A Scientist's Nightmare: Software Problem Leads to Five Retractions. Science, 314(5807), 1856-1857. Pattana, S. (2006).  ...  Software quality assurance Compromising on software quality can have severe consequences that can culminate in the retraction of published manuscripts (Miller, 2006) .  ... 
doi:10.5281/zenodo.5121618 fatcat:6bh256ynrbbwpkezniebwmtsie

The generic simulation cell method for developing extensible, efficient and readable parallel computational models

I. Honkonen
2014 Geoscientific Model Development Discussions  
This is an advantage for the development and testing of computational modeling software as each submodel can be developed and tested independently and subsequently used without modification in a more complex  ...  Support for parallel programming is also provided by allowing users to select which simulation variables to transfer between processes via a Message Passing Interface library.  ...  scientist's nightmare: software problem leads to five retractions, Science, 314, 15 1856-1857, doi:10.1126/science.314.5807.1856, 2006. 4579 Musser, D.  ... 
doi:10.5194/gmdd-7-4577-2014 fatcat:jsljxmfkarfglc2n4ncijgyn3q

Pfern/Osodos V1.0.0 [article]

Rutger Vos, Pedro Fernandes
2017 Zenodo  
or longitude_dec , which would be a nightmare if we try to merge our tables automatically in a script that is not programmed to "know" that these are equivalent.  ...  To a large extent, the problems of lack of protection arise from the inadequacy of legislation.  ... 
doi:10.5281/zenodo.1015287 fatcat:lb2a6harz5dprl2swnb6ixuyzu

The Past, Present and Future of Open Access [chapter]

Syed Shan e Ali Zaidi
2018 The Global Benefits of Open Research  
to those codes and software.  ...  Access to these resources and intellectual properties liberates the scientists from any limitations. Thus, a scientist's work is now unconfined.  ... 
doi:10.3390/books978-3-03897-010-1-11 fatcat:tuw4lr7tqvbczf2pgdbptxp6qi

Nonstandard Finite Difference Schemes

Ronald E. Mickens
2018 Notices of the American Mathematical Society  
Vergara from Politecnico di Milano, and A. Manzoni from EPFL are gratefully acknowledged. Mathematical Modeling, Analysis and Applications in  ...  We discovered these results unexpectedly when studying a more general family of polytopes. Acknowledgments The contributions of EPFL MEDIACOM, L. Dedè and C.  ...  Cardiovascular problems may lead to malfunction, disease, or death.  ... 
doi:10.1090/noti1617 fatcat:nzhfdj7fsncndnhfiaegkizvue

Enabling Reproducible Research: Open Licensing for Scientific Innovation

Victoria C. Stodden
US copyright law is a barrier to the sharing of scientific scholarship since it establishes exclusive rights for creators over their work, thereby limiting the ability of others to copy, use, build upon  ...  There is a gap in the current licensing and copyright structure for the growing number of scientists releasing their research publicly, particularly on the Internet.  ...  "A Scientist's Nightmare: Software Problem Leads to Five Retractions" Science, Vol 314, Dec 22 2006. 7 Robert Gentleman and D. T.  ... 
doi:10.7916/d8n01h1z fatcat:h7l5hyk5yrgh3mg3dibnoc4baq

Can Cyberspace potentially harm democracy and world stability? [chapter]

Basie von Solms, University of Johannesburg
2019 Moral Issues in the Natural Sciences and Technologies  
Acknowledgement I am deeply indebted to Paulu Joubert (2018) and Matthew van Zyl (2014) for access to their unpublished theses 'The forgotten experience: Human alienation from nature' (Pierre Joubert  ...  Without their kindness and assistance, this chapter would have been nearly impossible to produce.  ...  Ought a surgeon to kill one healthy person to save five by transplanting his or her healthy organs into the five patients each needing a separate organ?  ... 
doi:10.4102/aosis.2019.bk114.09 fatcat:gaub27xrsfaq7fsyya7lsne5gy

JSE 24:4 Full Version

Various Authors
2011 Journal of Scientific Exploration  
Lance Storm for kindly providing a reprint of an earlier article, and to Dr.  ...  Acknowledgments The authors wish to thank T. G. for providing assistance in fi nding interested individuals to serve as sitters in the experiment, A.  ...  Students serving honestly and cooperatively as participants for a scientist's research project hardly deserve to be looked upon with generalized suspicion.  ... 
doaj:52cd5afa18654845bdfa6ac56c143672 fatcat:g5ah5l5wf5hsrh7nyodd23njky
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